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Sequence, Chains, Asymmetric and Biological Units

Title STRUCTURAL BASIS FOR RNA UNWINDING BY THE DEAD-BOX PROTEIN DROSOPHILA VASA
Keywords DEAD-BOX, HELICASE, PROTEIN-RNA COMPLEX, ATPASE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, HYDROLASE/RNA COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   2DB3     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  DNA/RNA    E 7 105 0
2  RNA    F 7 129 0
3  RNA    G 7 137 0
4  RNA    H 6 117 0
5  Protein   ATP-DEPENDENT RNA HELICASE VASA  A 420 3296 0
6  Protein   ATP-DEPENDENT RNA HELICASE VASA  B 420 3296 0
7  Protein   ATP-DEPENDENT RNA HELICASE VASA  C 420 3296 0
8  Protein   ATP-DEPENDENT RNA HELICASE VASA  D 420 3296 0
9  Ligand   ATP-DEPENDENT RNA HELICASE VASA  A 2 0 32
10  Ligand   ATP-DEPENDENT RNA HELICASE VASA  B 2 0 32
11  Ligand   ATP-DEPENDENT RNA HELICASE VASA  C 2 0 32
12  Ligand   ATP-DEPENDENT RNA HELICASE VASA  D 2 0 32
13 Water     1319 0 1319
total       3034 13672 1447
Proteins
Unit 5 TYR202 ILE203 PRO204 PRO205 GLU206 PRO207 SER208 ASN209 ASP210 ALA211 ILE212 GLU213 ILE214 PHE215 SER216 SER217 GLY218 ILE219 ALA220 SER221 GLY222 ILE223 HIS224 PHE225 SER226 LYS227 TYR228 ASN229 ASN230 ILE231 PRO232 VAL233 LYS234 VAL235 THR236 GLY237 SER238 ASP239 VAL240 PRO241 GLN242 PRO243 ILE244 GLN245 HIS246 PHE247 THR248 SER249 ALA250 ASP251 LEU252 ARG253 ASP254 ILE255 ILE256 ILE257 ASP258 ASN259 VAL260 ASN261 LYS262 SER263 GLY264 TYR265 LYS266 ILE267 PRO268 THR269 PRO270 ILE271 GLN272 LYS273 CYS274 SER275 ILE276 PRO277 VAL278 ILE279 SER280 SER281 GLY282 ARG283 ASP284 LEU285 MET286 ALA287 CYS288 ALA289 GLN290 THR291 GLY292 SER293 GLY294 LYS295 THR296 ALA297 ALA298 PHE299 LEU300 LEU301 PRO302 ILE303 LEU304 SER305 LYS306 LEU307 LEU308 GLU309 ASP310 PRO311 HIS312 GLU313 LEU314 GLU315 LEU316 GLY317 ARG318 PRO319 GLN320 VAL321 VAL322 ILE323 VAL324 SER325 PRO326 THR327 ARG328 GLU329 LEU330 ALA331 ILE332 GLN333 ILE334 PHE335 ASN336 GLU337 ALA338 ARG339 LYS340 PHE341 ALA342 PHE343 GLU344 SER345 TYR346 LEU347 LYS348 ILE349 GLY350 ILE351 VAL352 TYR353 GLY354 GLY355 THR356 SER357 PHE358 ARG359 HIS360 GLN361 ASN362 GLU363 CYS364 ILE365 THR366 ARG367 GLY368 CYS369 HIS370 VAL371 VAL372 ILE373 ALA374 THR375 PRO376 GLY377 ARG378 LEU379 LEU380 ASP381 PHE382 VAL383 ASP384 ARG385 THR386 PHE387 ILE388 THR389 PHE390 GLU391 ASP392 THR393 ARG394 PHE395 VAL396 VAL397 LEU398 ASP399 GLU400 ALA401 ASP402 ARG403 MET404 LEU405 ASP406 MET407 GLY408 PHE409 SER410 GLU411 ASP412 MET413 ARG414 ARG415 ILE416 MET417 THR418 HIS419 VAL420 THR421 MET422 ARG423 PRO424 GLU425 HIS426 GLN427 THR428 LEU429 MET430 PHE431 SER432 ALA433 THR434 PHE435 PRO436 GLU437 GLU438 ILE439 GLN440 ARG441 MET442 ALA443 GLY444 GLU445 PHE446 LEU447 LYS448 ASN449 TYR450 VAL451 PHE452 VAL453 ALA454 ILE455 GLY456 ILE457 VAL458 GLY459 GLY460 ALA461 CYS462 SER463 ASP464 VAL465 LYS466 GLN467 THR468 ILE469 TYR470 GLU471 VAL472 ASN473 LYS474 TYR475 ALA476 LYS477 ARG478 SER479 LYS480 LEU481 ILE482 GLU483 ILE484 LEU485 SER486 GLU487 GLN488 ALA489 ASP490 GLY491 THR492 ILE493 VAL494 PHE495 VAL496 GLU497 THR498 LYS499 ARG500 GLY501 ALA502 ASP503 PHE504 LEU505 ALA506 SER507 PHE508 LEU509 SER510 GLU511 LYS512 GLU513 PHE514 PRO515 THR516 THR517 SER518 ILE519 HIS520 GLY521 ASP522 ARG523 LEU524 GLN525 SER526 GLN527 ARG528 GLU529 GLN530 ALA531 LEU532 ARG533 ASP534 PHE535 LYS536 ASN537 GLY538 SER539 MET540 LYS541 VAL542 LEU543 ILE544 ALA545 THR546 SER547 VAL548 ALA549 SER550 ARG551 GLY552 LEU553 ASP554 ILE555 LYS556 ASN557 ILE558 LYS559 HIS560 VAL561 ILE562 ASN563 TYR564 ASP565 MET566 PRO567 SER568 LYS569 ILE570 ASP571 ASP572 TYR573 VAL574 HIS575 ARG576 ILE577 GLY578 ARG579 THR580 GLY581 ARG582 VAL583 GLY584 ASN585 ASN586 GLY587 ARG588 ALA589 THR590 SER591 PHE592 PHE593 ASP594 PRO595 GLU596 LYS597 ASP598 ARG599 ALA600 ILE601 ALA602 ALA603 ASP604 LEU605 VAL606 LYS607 ILE608 LEU609 GLU610 GLY611 SER612 GLY613 GLN614 THR615 VAL616 PRO617 ASP618 PHE619 LEU620 ARG621
Unit 6 TYR202 ILE203 PRO204 PRO205 GLU206 PRO207 SER208 ASN209 ASP210 ALA211 ILE212 GLU213 ILE214 PHE215 SER216 SER217 GLY218 ILE219 ALA220 SER221 GLY222 ILE223 HIS224 PHE225 SER226 LYS227 TYR228 ASN229 ASN230 ILE231 PRO232 VAL233 LYS234 VAL235 THR236 GLY237 SER238 ASP239 VAL240 PRO241 GLN242 PRO243 ILE244 GLN245 HIS246 PHE247 THR248 SER249 ALA250 ASP251 LEU252 ARG253 ASP254 ILE255 ILE256 ILE257 ASP258 ASN259 VAL260 ASN261 LYS262 SER263 GLY264 TYR265 LYS266 ILE267 PRO268 THR269 PRO270 ILE271 GLN272 LYS273 CYS274 SER275 ILE276 PRO277 VAL278 ILE279 SER280 SER281 GLY282 ARG283 ASP284 LEU285 MET286 ALA287 CYS288 ALA289 GLN290 THR291 GLY292 SER293 GLY294 LYS295 THR296 ALA297 ALA298 PHE299 LEU300 LEU301 PRO302 ILE303 LEU304 SER305 LYS306 LEU307 LEU308 GLU309 ASP310 PRO311 HIS312 GLU313 LEU314 GLU315 LEU316 GLY317 ARG318 PRO319 GLN320 VAL321 VAL322 ILE323 VAL324 SER325 PRO326 THR327 ARG328 GLU329 LEU330 ALA331 ILE332 GLN333 ILE334 PHE335 ASN336 GLU337 ALA338 ARG339 LYS340 PHE341 ALA342 PHE343 GLU344 SER345 TYR346 LEU347 LYS348 ILE349 GLY350 ILE351 VAL352 TYR353 GLY354 GLY355 THR356 SER357 PHE358 ARG359 HIS360 GLN361 ASN362 GLU363 CYS364 ILE365 THR366 ARG367 GLY368 CYS369 HIS370 VAL371 VAL372 ILE373 ALA374 THR375 PRO376 GLY377 ARG378 LEU379 LEU380 ASP381 PHE382 VAL383 ASP384 ARG385 THR386 PHE387 ILE388 THR389 PHE390 GLU391 ASP392 THR393 ARG394 PHE395 VAL396 VAL397 LEU398 ASP399 GLU400 ALA401 ASP402 ARG403 MET404 LEU405 ASP406 MET407 GLY408 PHE409 SER410 GLU411 ASP412 MET413 ARG414 ARG415 ILE416 MET417 THR418 HIS419 VAL420 THR421 MET422 ARG423 PRO424 GLU425 HIS426 GLN427 THR428 LEU429 MET430 PHE431 SER432 ALA433 THR434 PHE435 PRO436 GLU437 GLU438 ILE439 GLN440 ARG441 MET442 ALA443 GLY444 GLU445 PHE446 LEU447 LYS448 ASN449 TYR450 VAL451 PHE452 VAL453 ALA454 ILE455 GLY456 ILE457 VAL458 GLY459 GLY460 ALA461 CYS462 SER463 ASP464 VAL465 LYS466 GLN467 THR468 ILE469 TYR470 GLU471 VAL472 ASN473 LYS474 TYR475 ALA476 LYS477 ARG478 SER479 LYS480 LEU481 ILE482 GLU483 ILE484 LEU485 SER486 GLU487 GLN488 ALA489 ASP490 GLY491 THR492 ILE493 VAL494 PHE495 VAL496 GLU497 THR498 LYS499 ARG500 GLY501 ALA502 ASP503 PHE504 LEU505 ALA506 SER507 PHE508 LEU509 SER510 GLU511 LYS512 GLU513 PHE514 PRO515 THR516 THR517 SER518 ILE519 HIS520 GLY521 ASP522 ARG523 LEU524 GLN525 SER526 GLN527 ARG528 GLU529 GLN530 ALA531 LEU532 ARG533 ASP534 PHE535 LYS536 ASN537 GLY538 SER539 MET540 LYS541 VAL542 LEU543 ILE544 ALA545 THR546 SER547 VAL548 ALA549 SER550 ARG551 GLY552 LEU553 ASP554 ILE555 LYS556 ASN557 ILE558 LYS559 HIS560 VAL561 ILE562 ASN563 TYR564 ASP565 MET566 PRO567 SER568 LYS569 ILE570 ASP571 ASP572 TYR573 VAL574 HIS575 ARG576 ILE577 GLY578 ARG579 THR580 GLY581 ARG582 VAL583 GLY584 ASN585 ASN586 GLY587 ARG588 ALA589 THR590 SER591 PHE592 PHE593 ASP594 PRO595 GLU596 LYS597 ASP598 ARG599 ALA600 ILE601 ALA602 ALA603 ASP604 LEU605 VAL606 LYS607 ILE608 LEU609 GLU610 GLY611 SER612 GLY613 GLN614 THR615 VAL616 PRO617 ASP618 PHE619 LEU620 ARG621
Unit 7 TYR202 ILE203 PRO204 PRO205 GLU206 PRO207 SER208 ASN209 ASP210 ALA211 ILE212 GLU213 ILE214 PHE215 SER216 SER217 GLY218 ILE219 ALA220 SER221 GLY222 ILE223 HIS224 PHE225 SER226 LYS227 TYR228 ASN229 ASN230 ILE231 PRO232 VAL233 LYS234 VAL235 THR236 GLY237 SER238 ASP239 VAL240 PRO241 GLN242 PRO243 ILE244 GLN245 HIS246 PHE247 THR248 SER249 ALA250 ASP251 LEU252 ARG253 ASP254 ILE255 ILE256 ILE257 ASP258 ASN259 VAL260 ASN261 LYS262 SER263 GLY264 TYR265 LYS266 ILE267 PRO268 THR269 PRO270 ILE271 GLN272 LYS273 CYS274 SER275 ILE276 PRO277 VAL278 ILE279 SER280 SER281 GLY282 ARG283 ASP284 LEU285 MET286 ALA287 CYS288 ALA289 GLN290 THR291 GLY292 SER293 GLY294 LYS295 THR296 ALA297 ALA298 PHE299 LEU300 LEU301 PRO302 ILE303 LEU304 SER305 LYS306 LEU307 LEU308 GLU309 ASP310 PRO311 HIS312 GLU313 LEU314 GLU315 LEU316 GLY317 ARG318 PRO319 GLN320 VAL321 VAL322 ILE323 VAL324 SER325 PRO326 THR327 ARG328 GLU329 LEU330 ALA331 ILE332 GLN333 ILE334 PHE335 ASN336 GLU337 ALA338 ARG339 LYS340 PHE341 ALA342 PHE343 GLU344 SER345 TYR346 LEU347 LYS348 ILE349 GLY350 ILE351 VAL352 TYR353 GLY354 GLY355 THR356 SER357 PHE358 ARG359 HIS360 GLN361 ASN362 GLU363 CYS364 ILE365 THR366 ARG367 GLY368 CYS369 HIS370 VAL371 VAL372 ILE373 ALA374 THR375 PRO376 GLY377 ARG378 LEU379 LEU380 ASP381 PHE382 VAL383 ASP384 ARG385 THR386 PHE387 ILE388 THR389 PHE390 GLU391 ASP392 THR393 ARG394 PHE395 VAL396 VAL397 LEU398 ASP399 GLU400 ALA401 ASP402 ARG403 MET404 LEU405 ASP406 MET407 GLY408 PHE409 SER410 GLU411 ASP412 MET413 ARG414 ARG415 ILE416 MET417 THR418 HIS419 VAL420 THR421 MET422 ARG423 PRO424 GLU425 HIS426 GLN427 THR428 LEU429 MET430 PHE431 SER432 ALA433 THR434 PHE435 PRO436 GLU437 GLU438 ILE439 GLN440 ARG441 MET442 ALA443 GLY444 GLU445 PHE446 LEU447 LYS448 ASN449 TYR450 VAL451 PHE452 VAL453 ALA454 ILE455 GLY456 ILE457 VAL458 GLY459 GLY460 ALA461 CYS462 SER463 ASP464 VAL465 LYS466 GLN467 THR468 ILE469 TYR470 GLU471 VAL472 ASN473 LYS474 TYR475 ALA476 LYS477 ARG478 SER479 LYS480 LEU481 ILE482 GLU483 ILE484 LEU485 SER486 GLU487 GLN488 ALA489 ASP490 GLY491 THR492 ILE493 VAL494 PHE495 VAL496 GLU497 THR498 LYS499 ARG500 GLY501 ALA502 ASP503 PHE504 LEU505 ALA506 SER507 PHE508 LEU509 SER510 GLU511 LYS512 GLU513 PHE514 PRO515 THR516 THR517 SER518 ILE519 HIS520 GLY521 ASP522 ARG523 LEU524 GLN525 SER526 GLN527 ARG528 GLU529 GLN530 ALA531 LEU532 ARG533 ASP534 PHE535 LYS536 ASN537 GLY538 SER539 MET540 LYS541 VAL542 LEU543 ILE544 ALA545 THR546 SER547 VAL548 ALA549 SER550 ARG551 GLY552 LEU553 ASP554 ILE555 LYS556 ASN557 ILE558 LYS559 HIS560 VAL561 ILE562 ASN563 TYR564 ASP565 MET566 PRO567 SER568 LYS569 ILE570 ASP571 ASP572 TYR573 VAL574 HIS575 ARG576 ILE577 GLY578 ARG579 THR580 GLY581 ARG582 VAL583 GLY584 ASN585 ASN586 GLY587 ARG588 ALA589 THR590 SER591 PHE592 PHE593 ASP594 PRO595 GLU596 LYS597 ASP598 ARG599 ALA600 ILE601 ALA602 ALA603 ASP604 LEU605 VAL606 LYS607 ILE608 LEU609 GLU610 GLY611 SER612 GLY613 GLN614 THR615 VAL616 PRO617 ASP618 PHE619 LEU620 ARG621
Unit 8 TYR202 ILE203 PRO204 PRO205 GLU206 PRO207 SER208 ASN209 ASP210 ALA211 ILE212 GLU213 ILE214 PHE215 SER216 SER217 GLY218 ILE219 ALA220 SER221 GLY222 ILE223 HIS224 PHE225 SER226 LYS227 TYR228 ASN229 ASN230 ILE231 PRO232 VAL233 LYS234 VAL235 THR236 GLY237 SER238 ASP239 VAL240 PRO241 GLN242 PRO243 ILE244 GLN245 HIS246 PHE247 THR248 SER249 ALA250 ASP251 LEU252 ARG253 ASP254 ILE255 ILE256 ILE257 ASP258 ASN259 VAL260 ASN261 LYS262 SER263 GLY264 TYR265 LYS266 ILE267 PRO268 THR269 PRO270 ILE271 GLN272 LYS273 CYS274 SER275 ILE276 PRO277 VAL278 ILE279 SER280 SER281 GLY282 ARG283 ASP284 LEU285 MET286 ALA287 CYS288 ALA289 GLN290 THR291 GLY292 SER293 GLY294 LYS295 THR296 ALA297 ALA298 PHE299 LEU300 LEU301 PRO302 ILE303 LEU304 SER305 LYS306 LEU307 LEU308 GLU309 ASP310 PRO311 HIS312 GLU313 LEU314 GLU315 LEU316 GLY317 ARG318 PRO319 GLN320 VAL321 VAL322 ILE323 VAL324 SER325 PRO326 THR327 ARG328 GLU329 LEU330 ALA331 ILE332 GLN333 ILE334 PHE335 ASN336 GLU337 ALA338 ARG339 LYS340 PHE341 ALA342 PHE343 GLU344 SER345 TYR346 LEU347 LYS348 ILE349 GLY350 ILE351 VAL352 TYR353 GLY354 GLY355 THR356 SER357 PHE358 ARG359 HIS360 GLN361 ASN362 GLU363 CYS364 ILE365 THR366 ARG367 GLY368 CYS369 HIS370 VAL371 VAL372 ILE373 ALA374 THR375 PRO376 GLY377 ARG378 LEU379 LEU380 ASP381 PHE382 VAL383 ASP384 ARG385 THR386 PHE387 ILE388 THR389 PHE390 GLU391 ASP392 THR393 ARG394 PHE395 VAL396 VAL397 LEU398 ASP399 GLU400 ALA401 ASP402 ARG403 MET404 LEU405 ASP406 MET407 GLY408 PHE409 SER410 GLU411 ASP412 MET413 ARG414 ARG415 ILE416 MET417 THR418 HIS419 VAL420 THR421 MET422 ARG423 PRO424 GLU425 HIS426 GLN427 THR428 LEU429 MET430 PHE431 SER432 ALA433 THR434 PHE435 PRO436 GLU437 GLU438 ILE439 GLN440 ARG441 MET442 ALA443 GLY444 GLU445 PHE446 LEU447 LYS448 ASN449 TYR450 VAL451 PHE452 VAL453 ALA454 ILE455 GLY456 ILE457 VAL458 GLY459 GLY460 ALA461 CYS462 SER463 ASP464 VAL465 LYS466 GLN467 THR468 ILE469 TYR470 GLU471 VAL472 ASN473 LYS474 TYR475 ALA476 LYS477 ARG478 SER479 LYS480 LEU481 ILE482 GLU483 ILE484 LEU485 SER486 GLU487 GLN488 ALA489 ASP490 GLY491 THR492 ILE493 VAL494 PHE495 VAL496 GLU497 THR498 LYS499 ARG500 GLY501 ALA502 ASP503 PHE504 LEU505 ALA506 SER507 PHE508 LEU509 SER510 GLU511 LYS512 GLU513 PHE514 PRO515 THR516 THR517 SER518 ILE519 HIS520 GLY521 ASP522 ARG523 LEU524 GLN525 SER526 GLN527 ARG528 GLU529 GLN530 ALA531 LEU532 ARG533 ASP534 PHE535 LYS536 ASN537 GLY538 SER539 MET540 LYS541 VAL542 LEU543 ILE544 ALA545 THR546 SER547 VAL548 ALA549 SER550 ARG551 GLY552 LEU553 ASP554 ILE555 LYS556 ASN557 ILE558 LYS559 HIS560 VAL561 ILE562 ASN563 TYR564 ASP565 MET566 PRO567 SER568 LYS569 ILE570 ASP571 ASP572 TYR573 VAL574 HIS575 ARG576 ILE577 GLY578 ARG579 THR580 GLY581 ARG582 VAL583 GLY584 ASN585 ASN586 GLY587 ARG588 ALA589 THR590 SER591 PHE592 PHE593 ASP594 PRO595 GLU596 LYS597 ASP598 ARG599 ALA600 ILE601 ALA602 ALA603 ASP604 LEU605 VAL606 LYS607 ILE608 LEU609 GLU610 GLY611 SER612 GLY613 GLN614 THR615 VAL616 PRO617 ASP618 PHE619 LEU620 ARG621
Nucleic acids
Unit 1 U1 U2 U3 U4 U5 U6 U7
Unit 2 U1 U2 U3 U4 U5 U6 U7
Unit 3 U1 U2 U3 U4 U5 U6 U7
Unit 4 U2 U3 U4 U5 U6 U7
Ligands
Unit 9 MG2801 ANP2901
Unit 10 MG2802 ANP2902
Unit 11 MG2803 ANP2903
Unit 12 MG2804 ANP2904
Chirality of ribose and phosphate atoms

Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany